Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

Freesurfer with infarct patients
by Budge, Mariana 03 Sep '17

03 Sep '17

Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana

3 10

Re: [Freesurfer] Pial surface editing
by Michelle VanTieghem 25 Aug '17

25 Aug '17

Hi, Yes, I am trying to use skull stripping from another package, since -gcut option did not work on our data for appropriate skull stripping, and as a result there is too much pial matter included as white matter. a) Is brainmask.mgz an appropriate input file for recon-all -all? for example, should I run "recon-all -all -i brainmask.mgz -s SB001" ? or, am I still using the original .dcm file as input, and merely putting a copy of my skull stripped brain into the SUB/mri directory that was created in the previous processing attempt? b) I am not understanding why i will still run skull stripping in the script here, if it is already done. Is the brainmask.auto.mgz generated just another duplicate copy that will be ignored for the actual segmentations? Will this still perform intensity normalization and other auto-recon1 steps normally? Thank you, Michelle On Tue, Jul 18, 2017 at 12:44 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Michelle > > can you cc the list so others can answers? I'm also no longer sure which > thread this is - were you trying to use the skull stripping from another > package? If so, convert that file to be named brainmask.mgz, then do *not* > include the -noskullstrip in your command line. Let us do the skull > strippping, which will create a brainmask.auto.mgz, but should preserve the > brainmask.mgz (since it is different than the .auto file) > > cheers > Bruce > > > > On Tue, 18 Jul 2017, Michelle VanTieghem wrote: > > >> Hi Bruce, >> >> >> Thanks for the information. Sorry I had changed my mail settings so I >> wasn’t >> seeing your responses until now. I had tried to run all, but just >> skip skull >> strip step, as well as the talaraich check step since we saw errors with >> that too. >> >> The command I used is follows: >> >> recon-all -all -3T -mprage -notal-check -noskullstrip >> -i/vega/psych/users/mrv2115/fsdata/ORIG_AFNI_SKULLSTRIP/SB00 >> 1/mprage_deobliqu >> e_brain.nii -s SB001 >> >> However, I am getting the following error during the registration step >> (see >> below). It looks like the mask volume brainmask.mgz hasn't been generated, >> but i don't know why. You suggested to convert my afni skull stripped >> brain >> to brain mask.mgz and place in the MRI folder. but am I still going to run >> the steps of autorecon-1 ? (intensity normalization, etc)? Does recon-all >> take inputs of already existing mri/brainmask.mgz files? It seems like it >> just needs one file and then re-generates a new directory with mri, >> scripts, >> ect. I would appreciate more detail on how to implement this! >> >> Thank you, >> >> Michelle >> >> >> ERROR: >> >> >> >> ======= NUMBER OF OPENMP THREADS = 1 ======= >> >> aligning to atlas containing skull, setting unknown_nbr_spacing = 3 >> >> using MR volume brainmask.mgz to mask input volume... >> >> reading 1 input volumes... >> >> logging results to talairach.log >> >> reading '/vega/psych/app/freesurfer/average/RB_all_2008-03-26.gca'... >> >> average std = 6.9 using min determinant for regularization = 4.7 >> >> 0 singular and 1812 ill-conditioned covariance matrices regularized >> >> reading 'nu.mgz'... >> >> mghRead(/vega/psych/users/mrv2115/fsdata/processed/SB001/ >> mri/brainmask.mgz, >> -1): could not $ >> >> mri_em_register: could not open mask volume brainmask.mgz. >> >> >> Linux bogota.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 >> 00:53:17 EST 2017 x86_$ >> >> >> recon-all -s SB001 exited with ERRORS at Tue Jul 18 11:50:24 EDT 2017 >> >> >> —— >> >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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Using own parcellation atlas
by Julie Hall 17 Aug '17

17 Aug '17

Hi experts, I would like to use a different atlas other than the 'default' Freesurfer atlases, namely the Gordon Parcellation (surface based parcellation of 333 ROIs of the cortex) to segment my T1 datasets. So I can go on to use these segmentations for DTI connectome analysis using MRTrix (or MatLab). I have two questions: - I have this atlas as a nifti file. Do I need to transform this atlas into a different file for it to run in freesurfer? - Can I run this step in autorecon3 (step 28)? Or should I rerun recon-all all together? If so, could you help me with what commands I need to run (mris_ca_train?)” Thank you, Julie

3 5

SPC in surface area
by Maria A Infante 15 Aug '17

15 Aug '17

Hi everyone, I have a questions concerning the SPC values for an individual brain region. I am looking at group differences (3 groups) in SPC in surface and found one region that was significant after correcting for multiple comparisons. I want to follow up with pairwise comparisons. Is there a way to extract the SPC values for that particular region? Are these the same values as the ones on the stack file? Thanks, Alejandra

4 4

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing
by Elijah Mak 03 Aug '17

03 Aug '17

Hi ZK, Thanks. It is great news! I would like to report the following. asegstats2table seems to be acting strangely. File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Even typing asegstats2table --help leads to the same error message. It was not found in a prev dev built or in 5.3. Thanks. Also, not sure if it's placebo, but freeview seems to be running quicker now. Best Wishes, Elijah

4 3

Medial Surface Problem
by Bronwyn Overs 03 Aug '17

03 Aug '17

Hi mailing list, I am currently processing a longitudinal image and have come across a problem at the medial surface in the long image (step 3). As you can see in the attached image, the rh medial surface has been significantly overestimated and extends into the lh surface. This error showed up only in only 1 of the 2 long images for this subject, and both the time-point images and the base are perfectly fine. Do you know why this is happening? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

4 19

Univariate Linear Mixed Effects
by Worker, Amanda 03 Aug '17

03 Aug '17

Hi there, I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could you explain why that is please? And also what hypotheses these three different contrasts are testing? C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)]; At the moment I have a simple design with two groups, 4-5 time points so I have a design matrix with 4 columns (intercept, weeks, group, group*time) and the contrast I am using is [0 0 0 1] to test the interaction term. If I were to add covariates such as age and gender would I simply add two more columns to my design matrix and contrast to look like this...[0 0 0 1 0 0]? Thanks in advance for your help. Amanda

2 2

reducing a matrix
by Linda Eva Heidinger 02 Aug '17

02 Aug '17

Dear experts in freesurfer, I myself am a very beginner in freesurfer but I come with a difficult question to answer. As you can see from the script below, I am trying to obtain the Bold in CVS35MNI152 template space which hopefully has better properties for accuracy and determination of location of a voxel for targeting in use with TMS. One can see that bbregister and mri_cvs_register were used followed by mri_vol2vol to register the Bold and transform it from subject space to the above template. Unfortunately, the template space is in freesurfer space (1mm^3,256^3) . When we try to run the result that we obtain after transformation in our AFNI programs, they couldn't run on our computers because of the size of the Bold matrix being too large. I am wondering if it is possible for mri_cvs_register to use a template that is of the same size as the T1? or really we should just somehow reformulate the transformation matrix resulting from mri_cvs_register which I believe is: final_CVSmorph_tocvs_avg35_MNI152.m3z to allow for a reduced final Bold matrix from mri_vol2vol which will have the same dimensions as the subject space which the original Bold had? I appreciate the time and attention you give this question. Thanks, -Linda ? # FreeSurfer commands nmr-std-env setenv SUBJECTS_DIR <path to the directory where all MRI data for this study reside> setenv SUBJECT <my subject code> cd $SUBJECTS_DIR # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual. recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4 # Second, do co-registration at the individual level between the hires anatomical and the bold (functional) image. # In the below example the already motion corrected (and otherwise preprocessed) bold data for run 005 are in # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii # Use boundary-based registration (bbregister) - this by far the most accurate tool. # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF 6 for within-subject registration. bbregister --mov $SUBJECT/bold/005/005.mc.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg boldregister.dat --fslmat ${SUBJECT}_anat2bold.mat # Just in case, let us make FSL type coregistration matrices as well. convert_xfm -omat ${SUBJECT}_bold2anat.mat -inverse ${SUBJECT}_anat2bold.mat # Now, we will compute a group-level coregistration from the individual brain to a template brain for both volumetric non-linear morphing. # We will use the standard brain cvs_avg35_inMNI152 as the target/template. mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECT/cvs_CVS35MNI152 --openmp 8 # Finally, we can move the bold image from the individual spac into the standard space: mri_vol2vol \ --mov $SUBJECT/bold/005/005.mc.nii \ --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \ --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ --noDefM3zPath \ --interp nearest \ --reg $SUBJECT/bold/boldregister.dat \ --no-save-reg \

3 5

error with fcseed-config & fcseed-sess
by Jessica Huang 02 Aug '17

02 Aug '17

Hi freesurfer experts, I’m using the fcseed-config and fcseed-sess commands to create a seed at V1 in accordance with the FsFastFunctionalConnectivity Walkthrough <http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth…> Steps: *STEP 4: Use fcseed-config to configure the parameters you wish to pass to your connectivity analysis. Sample command: fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold -mean -cfg mean.L_Posteriorcingulate.config *STEP 5: Create the FC seed for an individual fcseed-sess -s sessionid -cfg L_Posteriorcingulate.config V1 corresponds to the number 400 in $FREESRUFER_HOME/FreeSurferColorLUT.txt. The subject session I’m running is B101. The data is rest data but I named the file bold. Overall, with this information specific to my data, I ran the following commands: INPUT $ fcseed-config -segid 400 -fcname V1.dat -fsd bold -mean -cfg mean.V1.config OUTPUT fcname is V1.dat fcseed-config done INPUT $ fcseed-sess -s B101 -cfg mean.V1.config OUTPUT Logfile is /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/log/fcseed-sess.V1.dat.log.B101 Wed Jul 26 12:27:17 EDT 2017 Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir /Applications/freesurfer/fsfast/bin/fcseed-sess -s B101 -cfg mean.V1.config freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Wed Jul 26 12:27:17 EDT 2017 Darwin Caramazza-Labs-Mac-Pro.local 16.6.0 Darwin Kernel Version 16.6.0: Fri Apr 14 16:21:16 PDT 2017; root:xnu-3789.60.24~6/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects cd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir /Applications/freesurfer/fsfast/bin/fcseed-sess -s B101 -cfg mean.V1.config freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c mri_label2vol --seg /Users/caramazzalab/Desktop/Jess/Subjects/B201_mprage/mri/aparc+aseg.mgz --reg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta --temp /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz --fillthresh .5 --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --pvf /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz PVF /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/template.nii.gz Outut Volume: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz Registration File: /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Users/caramazzalab/Desktop/Jess/Subjects $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.50000 -0.00000 -0.00000 56.00000; -0.00000 -0.00000 -0.50000 56.00000; -0.00000 0.45455 -0.00000 32.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8.8 nHits Thresh: 4.4 Loading registration from /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/register.dof6.lta regio_read_register: loading lta RegMat: -------- 0.99785 0.02664 0.05987 0.19449; -0.06077 0.03415 0.99757 -39.76084; -0.02453 0.99906 -0.03570 2.27075; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -0.49893 -0.01332 -0.02994 55.90276; 0.01227 -0.49953 0.01785 54.86462; -0.02762 0.01552 0.45344 13.92689; 0.00000 0.00000 0.00000 1.00000; PVF /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/pvf.nii.gz Computing PVF 8.8 mri_label2vol done mri_binarize --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --match 400 $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir cmdline mri_binarize.bin --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz --o /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --match 400 sysname Darwin hostname Caramazza-Labs-Mac-Pro.local machine x86_64 user caramazzalab input /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/seg.nii.gz frame 0 nErode3d 0 nErode2d 0 output /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz Binarizing based on matching values nMatch 1 0 400 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 802816 0.000000 mri_binarize done mri_segstats --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz --seg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --id 1 --sum /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum --avgwfvol /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --i /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz --seg /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz --id 1 --sum /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/junk.sum --avgwfvol /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/avgwf.mgh sysname Darwin hostname Caramazza-Labs-Mac-Pro.local machine x86_64 user caramazzalab UseRobust 0 Loading /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/tmp.fcseed-sess.47801/mask.nii.gz Loading /Users/caramazzalab/Desktop/Jess/V1_REST_STUDY/dicomdir/B101/bold/001/fmcpr.nii.gz Voxel Volume is 8.8 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 0 segmentations Using PrintSegStat Computing spatial average of each frame ERROR: no voxels found in segmentation I attached the error log below - any idea what happened? Is there something I can change in these commands to yield the timecourse of V1? These are all subjects 18+ years of age. What do you think? Thank you in advance, any and all feedback would be greatly appreciated. Thanks, Jess

3 9

FSFAST (plot-twf-sess)
by John Anderson 02 Aug '17

02 Aug '17

Dear Dr Greeve, I am new to FSFAST so I highly appreciate your response. I have resting state fMRI data and I am following the steps as reported in wiki. My questions is regarding motion evaluation. The attached figure is an output of "plot-twf-sess". 1. Given the plotted data can we say that including run 003 is more reliable that all the other runs? 2. In the attached figure the command "plot-twf-sess" provide the maximum and minimum motion for every run on Y axes. I am wondering if there is any way to create a cutoff value of motion parameters for all the runs in the study were data can be included/excluded depending on lower/upper than this cutoff? Thank you for help John

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Freesurfer July 2017